fastq_to_fasta
A template for creation of SeqAn3 apps, with a FASTQ to FASTA example app.
Classes | Functions | Variables
raptor::hibf Namespace Reference

Must be first include. More...

Classes

struct  build_data
 
struct  chopper_pack_record
 
struct  node_data
 

Functions

size_t bin_size_in_bits (build_arguments const &arguments, size_t const number_of_kmers_to_be_stored)
 
template<seqan3::data_layout data_layout_mode>
void chopper_build (build_arguments const &arguments)
 
void compute_kmers (robin_hood::unordered_flat_set< size_t > &kmers, build_arguments const &arguments, chopper_pack_record const &record)
 
template<seqan3::data_layout data_layout_mode>
seqan3::interleaved_bloom_filter construct_ibf (robin_hood::unordered_flat_set< size_t > &parent_kmers, robin_hood::unordered_flat_set< size_t > &kmers, size_t const number_of_bins, lemon::ListDigraph::Node const &node, build_data< data_layout_mode > &data, build_arguments const &arguments, bool is_root)
 
template<seqan3::data_layout data_layout_mode>
void create_ibfs_from_chopper_pack (build_data< data_layout_mode > &data, build_arguments const &arguments)
 
template<seqan3::data_layout data_layout_mode>
size_t hierarchical_build (robin_hood::unordered_flat_set< size_t > &parent_kmers, lemon::ListDigraph::Node const &current_node, build_data< data_layout_mode > &data, build_arguments const &arguments, bool is_root)
 
template<seqan3::data_layout data_layout_mode>
size_t initialise_max_bin_kmers (robin_hood::unordered_flat_set< size_t > &kmers, std::vector< int64_t > &ibf_positions, std::vector< int64_t > &filename_indices, lemon::ListDigraph::Node const &node, build_data< data_layout_mode > &data, build_arguments const &arguments)
 
void insert_into_ibf (robin_hood::unordered_flat_set< size_t > &parent_kmers, robin_hood::unordered_flat_set< size_t > const &kmers, size_t const number_of_bins, size_t const bin_index, seqan3::interleaved_bloom_filter<> &ibf, bool is_root)
 
void insert_into_ibf (build_arguments const &arguments, chopper_pack_record const &record, seqan3::interleaved_bloom_filter<> &ibf)
 
template<seqan3::data_layout data_layout_mode>
void loop_over_children (robin_hood::unordered_flat_set< size_t > &parent_kmers, seqan3::interleaved_bloom_filter<> &ibf, std::vector< int64_t > &ibf_positions, lemon::ListDigraph::Node const &current_node, build_data< data_layout_mode > &data, build_arguments const &arguments, bool is_root)
 
size_t parse_chopper_pack_header (lemon::ListDigraph &ibf_graph, lemon::ListDigraph::NodeMap< node_data > &node_map, std::istream &chopper_pack_file)
 
chopper_pack_record parse_chopper_pack_line (std::string const &current_line)
 
template<seqan3::data_layout data_layout_mode>
void read_chopper_pack_file (build_data< data_layout_mode > &data, std::string const &chopper_pack_filename)
 
template<seqan3::data_layout data_layout_mode>
void update_user_bins (build_data< data_layout_mode > &data, std::vector< int64_t > &filename_indices, chopper_pack_record const &record)
 
template void chopper_build< seqan3::data_layout::uncompressed > (build_arguments const &)
 
template void chopper_build< seqan3::data_layout::compressed > (build_arguments const &)
 
template seqan3::interleaved_bloom_filter construct_ibf< seqan3::data_layout::uncompressed > (robin_hood::unordered_flat_set< size_t > &, robin_hood::unordered_flat_set< size_t > &, size_t const, lemon::ListDigraph::Node const &, build_data< seqan3::data_layout::uncompressed > &, build_arguments const &, bool)
 
template seqan3::interleaved_bloom_filter construct_ibf< seqan3::data_layout::compressed > (robin_hood::unordered_flat_set< size_t > &, robin_hood::unordered_flat_set< size_t > &, size_t const, lemon::ListDigraph::Node const &, build_data< seqan3::data_layout::compressed > &, build_arguments const &, bool)
 
template void create_ibfs_from_chopper_pack< seqan3::data_layout::uncompressed > (build_data< seqan3::data_layout::uncompressed > &, build_arguments const &)
 
template void create_ibfs_from_chopper_pack< seqan3::data_layout::compressed > (build_data< seqan3::data_layout::compressed > &, build_arguments const &arguments)
 
template size_t hierarchical_build< seqan3::data_layout::uncompressed > (robin_hood::unordered_flat_set< size_t > &, lemon::ListDigraph::Node const &, build_data< seqan3::data_layout::uncompressed > &, build_arguments const &, bool)
 
template size_t hierarchical_build< seqan3::data_layout::compressed > (robin_hood::unordered_flat_set< size_t > &, lemon::ListDigraph::Node const &, build_data< seqan3::data_layout::compressed > &, build_arguments const &, bool)
 
template size_t initialise_max_bin_kmers< seqan3::data_layout::uncompressed > (robin_hood::unordered_flat_set< size_t > &, std::vector< int64_t > &, std::vector< int64_t > &, lemon::ListDigraph::Node const &, build_data< seqan3::data_layout::uncompressed > &, build_arguments const &)
 
template size_t initialise_max_bin_kmers< seqan3::data_layout::compressed > (robin_hood::unordered_flat_set< size_t > &, std::vector< int64_t > &, std::vector< int64_t > &, lemon::ListDigraph::Node const &, build_data< seqan3::data_layout::compressed > &, build_arguments const &)
 
template void loop_over_children< seqan3::data_layout::uncompressed > (robin_hood::unordered_flat_set< size_t > &, seqan3::interleaved_bloom_filter<> &, std::vector< int64_t > &, lemon::ListDigraph::Node const &, build_data< seqan3::data_layout::uncompressed > &, build_arguments const &, bool)
 
template void loop_over_children< seqan3::data_layout::compressed > (robin_hood::unordered_flat_set< size_t > &, seqan3::interleaved_bloom_filter<> &, std::vector< int64_t > &, lemon::ListDigraph::Node const &, build_data< seqan3::data_layout::compressed > &, build_arguments const &, bool)
 
template void read_chopper_pack_file< seqan3::data_layout::uncompressed > (build_data< seqan3::data_layout::uncompressed > &, std::string const &)
 
template void read_chopper_pack_file< seqan3::data_layout::compressed > (build_data< seqan3::data_layout::compressed > &, std::string const &)
 
template void update_user_bins< seqan3::data_layout::uncompressed > (build_data< seqan3::data_layout::uncompressed > &, std::vector< int64_t > &, chopper_pack_record const &)
 
template void update_user_bins< seqan3::data_layout::compressed > (build_data< seqan3::data_layout::compressed > &, std::vector< int64_t > &, chopper_pack_record const &)
 

Variables

constexpr std::string_view hibf_prefix {"HIGH_LEVEL_IBF"}
 
constexpr std::string_view merged_bin_prefix {"MERGED_BIN"}
 
constexpr std::string_view split_bin_prefix {"SPLIT_BIN"}
 
constexpr size_t merged_bin_prefix_length {merged_bin_prefix.size()}
 

Detailed Description

Must be first include.

Function Documentation

◆ bin_size_in_bits()

size_t raptor::hibf::bin_size_in_bits ( build_arguments const &  arguments,
size_t const  number_of_kmers_to_be_stored 
)

◆ chopper_build()

template<seqan3::data_layout data_layout_mode>
void raptor::hibf::chopper_build ( build_arguments const &  arguments)

◆ chopper_build< seqan3::data_layout::compressed >()

template void raptor::hibf::chopper_build< seqan3::data_layout::compressed > ( build_arguments const &  )

◆ chopper_build< seqan3::data_layout::uncompressed >()

template void raptor::hibf::chopper_build< seqan3::data_layout::uncompressed > ( build_arguments const &  )

◆ compute_kmers()

void raptor::hibf::compute_kmers ( robin_hood::unordered_flat_set< size_t > &  kmers,
build_arguments const &  arguments,
chopper_pack_record const &  record 
)

◆ construct_ibf()

template<seqan3::data_layout data_layout_mode>
seqan3::interleaved_bloom_filter raptor::hibf::construct_ibf ( robin_hood::unordered_flat_set< size_t > &  parent_kmers,
robin_hood::unordered_flat_set< size_t > &  kmers,
size_t const  number_of_bins,
lemon::ListDigraph::Node const &  node,
build_data< data_layout_mode > &  data,
build_arguments const &  arguments,
bool  is_root 
)

◆ construct_ibf< seqan3::data_layout::compressed >()

template seqan3::interleaved_bloom_filter raptor::hibf::construct_ibf< seqan3::data_layout::compressed > ( robin_hood::unordered_flat_set< size_t > &  ,
robin_hood::unordered_flat_set< size_t > &  ,
size_t const  ,
lemon::ListDigraph::Node const &  ,
build_data< seqan3::data_layout::compressed > &  ,
build_arguments const &  ,
bool   
)

◆ construct_ibf< seqan3::data_layout::uncompressed >()

template seqan3::interleaved_bloom_filter raptor::hibf::construct_ibf< seqan3::data_layout::uncompressed > ( robin_hood::unordered_flat_set< size_t > &  ,
robin_hood::unordered_flat_set< size_t > &  ,
size_t const  ,
lemon::ListDigraph::Node const &  ,
build_data< seqan3::data_layout::uncompressed > &  ,
build_arguments const &  ,
bool   
)

◆ create_ibfs_from_chopper_pack()

template<seqan3::data_layout data_layout_mode>
void raptor::hibf::create_ibfs_from_chopper_pack ( build_data< data_layout_mode > &  data,
build_arguments const &  arguments 
)

◆ create_ibfs_from_chopper_pack< seqan3::data_layout::compressed >()

template void raptor::hibf::create_ibfs_from_chopper_pack< seqan3::data_layout::compressed > ( build_data< seqan3::data_layout::compressed > &  ,
build_arguments const &  arguments 
)

◆ create_ibfs_from_chopper_pack< seqan3::data_layout::uncompressed >()

template void raptor::hibf::create_ibfs_from_chopper_pack< seqan3::data_layout::uncompressed > ( build_data< seqan3::data_layout::uncompressed > &  ,
build_arguments const &   
)

◆ hierarchical_build()

template<seqan3::data_layout data_layout_mode>
size_t raptor::hibf::hierarchical_build ( robin_hood::unordered_flat_set< size_t > &  parent_kmers,
lemon::ListDigraph::Node const &  current_node,
build_data< data_layout_mode > &  data,
build_arguments const &  arguments,
bool  is_root 
)

◆ hierarchical_build< seqan3::data_layout::compressed >()

template size_t raptor::hibf::hierarchical_build< seqan3::data_layout::compressed > ( robin_hood::unordered_flat_set< size_t > &  ,
lemon::ListDigraph::Node const &  ,
build_data< seqan3::data_layout::compressed > &  ,
build_arguments const &  ,
bool   
)

◆ hierarchical_build< seqan3::data_layout::uncompressed >()

template size_t raptor::hibf::hierarchical_build< seqan3::data_layout::uncompressed > ( robin_hood::unordered_flat_set< size_t > &  ,
lemon::ListDigraph::Node const &  ,
build_data< seqan3::data_layout::uncompressed > &  ,
build_arguments const &  ,
bool   
)

◆ initialise_max_bin_kmers()

template<seqan3::data_layout data_layout_mode>
size_t raptor::hibf::initialise_max_bin_kmers ( robin_hood::unordered_flat_set< size_t > &  kmers,
std::vector< int64_t > &  ibf_positions,
std::vector< int64_t > &  filename_indices,
lemon::ListDigraph::Node const &  node,
build_data< data_layout_mode > &  data,
build_arguments const &  arguments 
)

◆ initialise_max_bin_kmers< seqan3::data_layout::compressed >()

template size_t raptor::hibf::initialise_max_bin_kmers< seqan3::data_layout::compressed > ( robin_hood::unordered_flat_set< size_t > &  ,
std::vector< int64_t > &  ,
std::vector< int64_t > &  ,
lemon::ListDigraph::Node const &  ,
build_data< seqan3::data_layout::compressed > &  ,
build_arguments const &   
)

◆ initialise_max_bin_kmers< seqan3::data_layout::uncompressed >()

template size_t raptor::hibf::initialise_max_bin_kmers< seqan3::data_layout::uncompressed > ( robin_hood::unordered_flat_set< size_t > &  ,
std::vector< int64_t > &  ,
std::vector< int64_t > &  ,
lemon::ListDigraph::Node const &  ,
build_data< seqan3::data_layout::uncompressed > &  ,
build_arguments const &   
)

◆ insert_into_ibf() [1/2]

void raptor::hibf::insert_into_ibf ( build_arguments const &  arguments,
chopper_pack_record const &  record,
seqan3::interleaved_bloom_filter<> &  ibf 
)

◆ insert_into_ibf() [2/2]

void raptor::hibf::insert_into_ibf ( robin_hood::unordered_flat_set< size_t > &  parent_kmers,
robin_hood::unordered_flat_set< size_t > const &  kmers,
size_t const  number_of_bins,
size_t const  bin_index,
seqan3::interleaved_bloom_filter<> &  ibf,
bool  is_root 
)

◆ loop_over_children()

template<seqan3::data_layout data_layout_mode>
void raptor::hibf::loop_over_children ( robin_hood::unordered_flat_set< size_t > &  parent_kmers,
seqan3::interleaved_bloom_filter<> &  ibf,
std::vector< int64_t > &  ibf_positions,
lemon::ListDigraph::Node const &  current_node,
build_data< data_layout_mode > &  data,
build_arguments const &  arguments,
bool  is_root 
)

◆ loop_over_children< seqan3::data_layout::compressed >()

template void raptor::hibf::loop_over_children< seqan3::data_layout::compressed > ( robin_hood::unordered_flat_set< size_t > &  ,
seqan3::interleaved_bloom_filter<> &  ,
std::vector< int64_t > &  ,
lemon::ListDigraph::Node const &  ,
build_data< seqan3::data_layout::compressed > &  ,
build_arguments const &  ,
bool   
)

◆ loop_over_children< seqan3::data_layout::uncompressed >()

template void raptor::hibf::loop_over_children< seqan3::data_layout::uncompressed > ( robin_hood::unordered_flat_set< size_t > &  ,
seqan3::interleaved_bloom_filter<> &  ,
std::vector< int64_t > &  ,
lemon::ListDigraph::Node const &  ,
build_data< seqan3::data_layout::uncompressed > &  ,
build_arguments const &  ,
bool   
)

◆ parse_chopper_pack_header()

size_t raptor::hibf::parse_chopper_pack_header ( lemon::ListDigraph &  ibf_graph,
lemon::ListDigraph::NodeMap< node_data > &  node_map,
std::istream &  chopper_pack_file 
)

◆ parse_chopper_pack_line()

chopper_pack_record raptor::hibf::parse_chopper_pack_line ( std::string const &  current_line)

◆ read_chopper_pack_file()

template<seqan3::data_layout data_layout_mode>
void raptor::hibf::read_chopper_pack_file ( build_data< data_layout_mode > &  data,
std::string const &  chopper_pack_filename 
)

◆ read_chopper_pack_file< seqan3::data_layout::compressed >()

template void raptor::hibf::read_chopper_pack_file< seqan3::data_layout::compressed > ( build_data< seqan3::data_layout::compressed > &  ,
std::string const &   
)

◆ read_chopper_pack_file< seqan3::data_layout::uncompressed >()

template void raptor::hibf::read_chopper_pack_file< seqan3::data_layout::uncompressed > ( build_data< seqan3::data_layout::uncompressed > &  ,
std::string const &   
)

◆ update_user_bins()

template<seqan3::data_layout data_layout_mode>
void raptor::hibf::update_user_bins ( build_data< data_layout_mode > &  data,
std::vector< int64_t > &  filename_indices,
chopper_pack_record const &  record 
)

◆ update_user_bins< seqan3::data_layout::compressed >()

template void raptor::hibf::update_user_bins< seqan3::data_layout::compressed > ( build_data< seqan3::data_layout::compressed > &  ,
std::vector< int64_t > &  ,
chopper_pack_record const &   
)

◆ update_user_bins< seqan3::data_layout::uncompressed >()

template void raptor::hibf::update_user_bins< seqan3::data_layout::uncompressed > ( build_data< seqan3::data_layout::uncompressed > &  ,
std::vector< int64_t > &  ,
chopper_pack_record const &   
)

Variable Documentation

◆ hibf_prefix

constexpr std::string_view raptor::hibf::hibf_prefix {"HIGH_LEVEL_IBF"}
constexpr

◆ merged_bin_prefix

constexpr std::string_view raptor::hibf::merged_bin_prefix {"MERGED_BIN"}
constexpr

◆ merged_bin_prefix_length

constexpr size_t raptor::hibf::merged_bin_prefix_length {merged_bin_prefix.size()}
constexpr

◆ split_bin_prefix

constexpr std::string_view raptor::hibf::split_bin_prefix {"SPLIT_BIN"}
constexpr